We study theoretically two spatially separate quasi-one-dimensional atomic Fermi gases in a double-well trap. By tuning independently their spin polarizations, a Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) superfluid or a Bardeen-Cooper-Schrieffer (BCS) superfluid may be formed in each well. We seek the possibility of creating a spatially tunable atomic Josephson junction between two superfluids, which is supposed to be realizable via building a weak link at given positions of the double-well barrier. We show that within mean-field theory the maximum Josephson current is proportional to the order parameter in two wells. Thus, the spatial inhomogeneity of the FFLO order parameter in one well may be directly revealed through the current measurement with the position-tunable link. We anticipate that this type of Josephson measurement can provide useful evidence for the existence of exotic FFLO superfluids. Possible experimental realizations of the Josephson measurements in atomic Fermi gases are discussed.